Biclustering as a method for RNA local multiple sequence alignment.

ABSTRACT:

Motivations

Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address.

Results

We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing b

SUBMITTER: Wang S 

PROVIDER: S-EPMC2228335 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature